Selin Gerit, a London-based presenter for BBC's Turkish service, was until last week relatively unknown in her home country. However, that changed when Recep Tayyip Erdoğan told parliament she was guilty of treason over her coverage of the anti-government protests sweeping the nation.

The prime minister's condemnation has triggered concerns among fellow journalists, who believe Erdoğan – who accuses the media of fanning the demonstrations – is attempting to stifle dissent.

The campaign against Girit was launched last weekend when the mayor of Ankara, Melih Gökçek, posted a series of angry tweets. The BBC criticised what it called government intimidation. The corporation's comments triggered Erdoğan to claim in parliament the following day that Girit was "part of a conspiracy against her own country".

Turkish journalists see the focus on Girit as a warning to them all – an example to cow the rest of them into submission. Serdar Korucu, editor of a major domestic news outlet, said: "The prime minister is telling us, 'Be careful what you say and do, or you can easily be next'."

The mainstream media have ignored much of the unrest, with CNNTürk airing a documentary on penguins while the central square in Istanbul became the scene of street protests unprecedented in Erdoğan's 10-year rule. The public was outraged, and protests were staged outside local news outlets.

Many journalists, however, were not surprised. Fatma Demirelli, managing editor of Today's Zaman, the English-language daily, said self-censorship had long become the norm in newsrooms. "Journalists now have a sort of split brain: on the one hand you see what the news is, but on the other you immediately try to gauge how to report it without stepping on anyone's foot," she said. "Self-censorship has become an automatic reflex."

Turkey has more journalists in its prisons than anywhere else in the world, with 67 incarcerated, according to Reporters Without Borders. But the government's stance against the media has drawn more attention during the protests around Gezi Park.

"The significant difference with the current events is that the censorship has affected a different constituency of people – middle-class Turks – rather than other groups whose causes have been more frequently subjected to censorship, such as activists advocating Kurdish rights and politics," said Andrew Gardner, Turkey researcher for Amnesty International.

"Another difference is that the events were widely covered in international media, exposing the self-censorship in mainstream Turkish media further."

Censorship and control aside, violence and arbitrary threats against journalists trying to report the events have also increased. The Committee to Protect Journalists has documented a large number attacks on the press during the protests, including physical assault, detentions, threats and the unlawful confiscation of equipment and protective gear. Several reporters – Turkish and foreign – have sustained injuries from beatings and plastic bullets used by the police.

Erdoğan has accused Girit of being 'part of a conspiracy against her own country'. Photograph: Tolga Adanali/Depo Photos/Sipa Tolga Adanali/Depo Photos/SIPA

The organisation singled out police brutality as the biggest threat against journalists in Turkey, claiming that reporters were facing the greatest risk to their safety in more than two decades.

After covering a peaceful protest that was violently dispersed with teargas and water cannon, journalist Alpbugra Bahadir Gültekin was repeatedly beaten by the police. "I told them that I was with the press, but they first insulted and then started beating me. After I fell to the ground, several officers continued to beat and to kick me," he said.

He managed to recover CCTV footage of the incident and filed charges against the police. However, he does not expect to be heard. "They operate in an atmosphere of impunity. But we have to start somewhere, and bring these incidents to light, " Gültekin said.

Demirelli and Korucu agreed that Erdoğan was becoming a figure beyond criticism. "News stations have started to correct the prime minister's slips of the tongue unasked, in order to be on the safe side," Korucu said. "Nobody wants to ask uncomfortable questions, in order to keep him happy. But how can we begin to understand issues of interest if asking is not free any more?"

Demirelli said: "Journalists now always wonder if they really want to investigate, for fear that they might actually find something."